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Oh, thunderslide kit.

Great! So what you started with was a stock bike basically running at or within 800' of sea-level with Keihin #45 pilot jets and #180 main jets. And along with the other changes, it now has 'Thunderslide' #48 pilot jets and dynojet #185 main jets. I cannot identify Thunderslide pilot jet inlet diameters versus Keihin, so that will be impossible to determine what difference it makes to fueling. We'll also need to know the jet needle clip setting too, assuming the dynojet came with clipped position jet needles and those were installed along with the dynojet jets.

Okay, so this is what we have before the SuperTrapp Supermegs were installed:

Pilot Jet increase, Keihin #45 to a Dynojet/Thunderside #48 = ??? Probably greater than 6% increase in fuel.
Jet needle height change = unknown.
Main jet increase, Keihin #180 to Dynojet #185 is basically something in the area of a Keihin #209. (209-180)/180 = 16% more fuel being delivered.
Modifications to CI displacement = none
Modifications to piston compression ratio = none
Cam modifications = mid-range boosting S&S 551, when compression ratio is bumped up.
Air filter, Zippers.
Rider's impression with True Duals exhaust at this point is that they delivered more top-end than after those were swapped for the SuperTrapp 2:1 SuperMegs and that now the bike doesn't have much throttle response past 3,400 rpms with 6 diffusers and open cap. Diffusers are sooty.

Going off the modifications and the two comments, "bike doesn't have much throttle response past 3,400 RPMS and diffusers are sooty," seems to make sense to me as an average tuner and believer in the 3% rule. I could completely see any bike, not just your FLHTC falling on its face as the main jet kicks in, more-so the farther the bike gets from sea level. In my early tuning of my bike, after putting the SuperTrapp with 6 diffusers on and unchanged jets, I'd take it up to mountain summits. The higher I went the more top-end fell off, as was with the restrictive stock muffler. Same was true if my air filter was over oiled, when I'd open the throttle to pass cars, the bike wouldn't do it. My jetting was too rich. Probably below 13.0:1 on the AFR too rich, if I had to guess.

So I lowered my main jets and added more diffusers, experimenting with 8 to 10 plates. Okay, now the bike wasn't restricted on passing and did very well going over summits, but my mid-range at 10 plates wasn't as good as it was at 8.

I also skimmed through a bunch of HD forums where guys were tuning their 88 ci bikes or asking for advice. The HD Performance site was quite clear on how to tune for airflow mods and the various HD forum members who seemed to know it all mimicked that same advice; go one size up on the pilot jet and don't change much else. So in your case, with the SuperTrapp 2:1 Supermeg your main jet should be a #180 Keihin, your pilot jet should be a #48 Keihin at the very most and if anything, bump your jet needle up from the stock position by about 1mm (you might be able to get away with 2mm or slightly more with an 88ci). The jet needle will take advantage of S&S 551's better mid-range flow. The other Zipper and SuperTrapp airflow mods should take care of the #180 Keihin main, which will be flowing more mid-range fuel now because of the jn bump.

Instead, you're forcing 16.1% on your poor bike's top end and that's after you changed its cam from one that probably had better top-end than mid-range airflow performance. Which begs the question, and not to be critical, if you're knee-capping your top-end with the S&S 551, how is the engine suppose to deal with 16.1% more fuel on top (>3,400 RPMs)? This explains in my mind why you're getting poor top-end throttle performance and exhaust soot, more than anything negative to do with the SuperTrapp.

As for the number of plates to run and whether or not to use the closed-end cap, I'd read up, here and Google searching the Web, on what others have started with on their SuperTrapps and whether you prefer the open-end vs. closed-end sound, one way or another. From what I've read about HDs on the dyno, they produce more HP with the open cap or no cap. From what I know about the SuperTrapp closed-end cap, is that it can boost both, but not as bleeding edge on top-end. And since your bike's 551 cam is for mid-range, I'd start with the closed-end cap at about 12 - 15 diffusers, the jet settings as I mentioned above (sorry, the Dynojet kit and modifications made to the carbs, less the jet needle, have to go bye-bye), then experiment as the SuperTrapp FAQs recommend by swapping on or off two diffusers at a time and see how the bike performs.

Given the elevation then, stock jetting would make the three carb fuel circuits rich. Most bike repair manuals will have one line in them about altitude jetting, in that for continued operation above 4,000,' jet sizes should be reduced by 8%. That's per the manufacturer. So the stock #45 Keihin would be a 45/1.08= #42 Keihin, the jet needle should be set to stock (plunged to its lowest position), and main #180 Keihin changed to a 180/1.08= #168 Keihin. But that's for stock airflow, which yours is not and you're not quite that high up. I'd think with 88ci displacement, the bike would be more forgiving of a mixture that was a little rich here and there. But now, I'm convinced even more about my earlier observation. Running that dynojet #185 (equivalent to a Keihin #209) at your elevation would result in the exact symptoms you're experiencing.

BTW, for tinkering with jet sizes, dirt bike shops will usually let you trade in/out after buying a set. Ask about that. Most sell used jets right along with new ones. They know jet tuning is experimentation and besides, jets never wear out.

finally got it.....left the dynojet kit and thunderside in and changed the 185 main jet to a 175 and it improved changed the 48 pilot jet to a 45 and it improved more.. now running open end cap and 6 disc....the bottom, mid and top ranges are all good pulls like a train ... the mpg is up and the plugs have good color disc are a dark copper probably still a little rich but I prefer it that way thanks for all your help